1. Kandler, O., Weiss, N., Genus Lactobacillus Beijerinck 1901, 212A.L. In: Sneath, P.H.A., Mair, N.S., Sharpe, N.E., Holt, J.H. (Eds.), Bergey’s Manual of Systematic Bacteriology, vol. 2. Williams and Wilkins, Baltimore, pp. 1209e1234 (1986).
2. Hammes, W.P., Vogel, R.F., The genus Lactobacillus. In: Wood, B.J.B., Holzapfel, W.H. (Eds.), The Genera of Lactic Acid Bacteria, vol. 2. Blackie Academic and Professional, London, pp. 19e54, (1995).
3. Collins, M.D., Rodrigues, U.M., Ash, C., Aguirre, M., Farrow, J.A.E., Martinez- Murcia, A., Phillips, B.A., Williams, A.M., Wallbanks, S., Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol.
Lett. 77, 5e12 (1991).
4. Pot, B. The taxonomy of lactic acid bacteria. In: Corrieu, G., Luquet, F.M. (Eds.), Bacteries lactiques et De la génétique aux ferments. Lavoisier, Paris, (2008).
5. Pot, B., Tsakalidou, E. Taxonomy and metabolism of Lactobacillus. In: Ljungh, A., Wadstro¨m, T.
(Eds.), Lactobacillus Molecular Biology: From Genomics to Probiotics. Caister Academic Press, Norfolk, pp. 3e58, (2009).
6. de Vries, M., Vaughan, E., Kleerebezem, M., de Vos, W.M. Lactobacillus plantarum e survival, functional and potential probiotic properties in the human gastrointestinal tract. Int. Dairy J. 16, 1018e1028, (2006).
7. Leroy, F., De Vuyst, L. Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci. Technol. 15, 67e78, (2004).
8. FAO/WHO. Guidelines for the Evaluation of Probiotics in Food. Working group report. Food and Agricultural Organization of the United Nations and World Health Organization, London, Ontario, Canada, (2002).
9. Vanderhoof JA, Young RJ, Murray N, Kaufman SS. Treatment strategies for small bowel bacterial overgrowth in short bowel syndrome. J Pediatr Gastroenterol Nutr ;27:155–60, (1998).
10. Caplan, M.S. and Jilling, T. Neonatal Necrotizing Enterocolitis: Possible Role of Probiotic Supplementation. Journal of Pediatric Gastroenterology and Nutrition, 30, S18-S22, (2000).
87 11. Marteau, P.R., De Vrese, M., Cellier, C.J., Schrezenmeir, J. Protection from gastrointestinal diseases with the use of probiotics. Am. J. Clin. Nutr.73, 430e436, (2001).
12. Guandalini S, Pensabene L, Zikri MA, et al. Lactobacillus GG administered in oral rehydration solution to children with acute diarrhea: a multicenter European trial. J Pediatr Gastroenterol Nutr ;30:54–60, (2000).
13. Benchimol E.I., Mack D.R. Probiotics in relapsing and chronic diarrhea. J. Pediatr. Hematol. Oncol;
26:515–517, (2004).
14. Hilton E, Kolakowski P, Singer C, Smith M. Efficacy of Lactobacillus GG as a diarrheal preventive in travelers. J Travel Med; 4:41–3, (1997).
15. Saavedra JM, Bauman NA, Oung I, Perman JA, Yolken RH. Feeding of Bifidobacterium bifidum and Streptococcus thermophilus to infants in hospital for prevention of diahrroea and shedding of rotavirus. Lancet; 344:1046–9, (1994).
16) Salminen E, Elomaa I, Minkkinen J, Vapaatalo H, Salminen S. Preservation of intestinal integrity during radiotherapy using live Lactobacillus acidophilus cultures. Clin Radiol ;39 :4357, (1988).
17. DeSimone, C. The adjuvant effect of yogurt on gamma interferon by Con-A stimulated human lymphocytes. Nutr Rep Int 33, 419–433, (1986).
18. O’Sullivan, M.G., Thornton, G., O’Sullivan, G.C. and Collins, J.K. Probiotic bacteria: myth or reality.
Trends Food Sci Technol 3, 309–314, (1992).
19. Dodd, H.M. and Gasson, M.J. Bacteriocins of Lactic Acid Bacteria. In Genetics and Biotechnology of Lactic acid Bacteria ed. Gasson, M.J. and de Vos, W.M. pp. 211–251. Glasgow, UK: Blackie Academic and Professional, (1994).
20. del Miraglia, G.M. and De Luca, M.G. The role of probiotics in the clinical management of food allergy and atopic dermatitis. J Clin Gastroenterol 38, S84–S85, (2004).
21. Mucchetti, G., Neviani, E. Microbiologia e tecnologia lattiero-casearia. Qualita` e sicurezza. In:
Tecniche nuove (Ed.) Milan, Italy, (2006).
22. Neviani, E., De Dea Lindner, J., Bernini, V., Gatti, M. Recovery and differentiation of long ripened cheese microflora through a new cheese-based cultural medium. Food Microbiology 26, 240–245, (2009).
88 23. Beresford, T., Pelaez, C., Jimeno, J. Nature and growth of non-starter microflora. In Improvement of the Quality of the Production of Raw Milk Cheeses. Proceedings of the Symposium on Quality and Microbiology of Traditional and Raw Milk Cheeses. European Commission, Brussels, pp. 225–237, (1999).
24. Peterson, S.D., Marshall, R.T. Nonstarter lactobacilli in Cheddar cheese: a review. Journal of Dairy Science 73, 1395–1410, (1990).
25. Succi, M., Tremonte, P., Reale, A., Sorrentino, E., Grazia, L., Pacifico, S., Coppola, R. Bile salt and acid tolerance of Lactobacillus rhamnosus strains isolated from Parmigiano Reggiano cheese. FEMS Microbiology Letters 244 (1), 129–137, (2005).
26. De Dea Lindner, J., Bernini, V., De Lorentiis, A., Pecorari, A., Neviani, E., Gatti, M. Parmigiano Reggiano cheese: evolution of cultivable and total lactic microflora and peptidase activities during manufacture and ripening. Dairy Science Technology 88, 511–523, (2008).
27. Gatti, M., De Dea Lindner, J., De Lorentiis, A., Bottari, B., Santarelli, M., Bernini, V., Neviani, E.
Dynamics of whole and lysed bacterial cells during Parmigiano- Reggiano cheese production and ripening. Applied and Environmental Microbiology 74, 6161–6167, (2008).
28. Neubauer C, Gao YG, Andersen KR, Dunham CM, Kelley AC, et al. The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell 139:1084–95, (2009).
29. Christensen SK, Gerdes K. RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol. Microbiol. 48:1389–400, (2003).
30. Arcus, V.L.; Rainey, P.B.; Turner, S.J. The PIN-domain toxin–antitoxin array in mycobacteria.
Trends Microbiol., 13, 360–365, (2005).
31. Guo, Y.; Quiroga, C.; Chen, Q.; McAnulty, M.J.; Benedik, M.J.;Wood, T.K.;Wang, X. RalR (a DNase) and RalA (a small RNA) form a type I toxin–antitoxin system in Escherichia coli. Nucleic Acids Res, 42, 6448–6462 (2014).
32. Page, R.; Peti,W. Toxin-antitoxin systems in bacterial growth arrest and persistence. Nat. Chem.
Biol., 12, 208–214, (2016).
33. Ogura, T.; Hiraga, S. Mini-F plasmid genes that couple host cell division to plasmid proliferation.
Proc. Natl. Acad. Sci. USA, 80, 4784–4788, (1983).
89 34. Gerdes, K.; Rasmussen, P.B.; Molin, S. Unique type of plasmid maintenance function:
Postsegregational killing of plasmid-free cells. Proc. Natl. Acad. Sci. USA, 83, 3116–3120, (1986).
35. Van Melderen, L.; Saavedra de Bast, M. Bacterial toxin–antitoxin systems: More than selfish entities? PLoS Genet. (2009).
36. Coussens, N.P.; Daines, D.A. Wake me when it’s over—Bacterial toxin-antitoxin proteins and induced dormancy. Exp. Biol. Med., 241, 1332–1342, (2016).
37. Gerdes, K.; Christensen, S.K.; Lobner-Olesen, A. Prokaryotic toxin-antitoxin stress response loci.
Nat. Rev. Microbiol., 3, 371–382, (2005).
38. Wen, Y.; Behiels, E.; Devreese, B. Toxin–Antitoxin systems: Their role in persistence, biofilm formation, and pathogenicity. Pathog. Dis. 70, 240–249, (2014).
39. Pandey, D.P.; Gerdes, K. Toxin–antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res, 33, 966–976, (2005).
40. Robson, J.; McKenzie, J.L.; Cursons, R.; Cook, G.M.; Arcus, V.L. The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin–antitoxin module that controls growth via inhibition of translation. J. Mol. Biol, 390, 353–367, (2009).
41. Shao Y Harrison EM Bi D Tai C He X Ou H-Y Rajakumar K Deng Z. TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea. Nucleic Acids Res 39: D606–D611, (2011).
42. Yamaguchi Y Park J-H Inouye M. Toxin–antitoxin systems in bacteria and archaea. Annu Rev Genet 45: 61–79, (2011).
43. Ramage HR Connolly LE Cox JS. Comprehensive functional analysis of Mycobacterium tuberculosis toxin–antitoxin systems: implications for pathogenesis, stress responses, and evolution.
PLoS Genet 5: e1000767, (2009).
44. Hobby GL Meyer K Chaffee E. Observations on the mechanism of action of penicillin. Exp Biol Med 50: 281–285, (1942).
45. Bigger JW. Treatment of staphylococcal infections with penicillin. Lancet 244: 497–500, (1944).
46. Scherrer R Moyed HS. Conditional impairment of cell division and altered lethality in hipA mutants of Escherichia coli K-12. J Bacteriol 170: 3321–3326, (1988).
90 47. Moyed HS Bertrand KP. HipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 155: 768–775, (1983).
48. Moyed HS Broderick SH. Molecular cloning and expression of hipA, a gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J Bacteriol 166: 399–
403, (1986).
49. Balaban NQ Merrin J Chait R Kowalik L Leibler S. Bacterial persistence as a phenotypic switch.
Science 305: 1622–1625, (2004).
50. Kwan BW Valenta JA Benedik MJ Wood TK. Arrested protein synthesis increases persister-like cell formation. Antimicrob Agents Chemother 57: 1468–1473, (2013).
51. Wang X Wood TK. Toxin–antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 77: 5577–5583, (2011).
52. Black DS Kelly AJ Mardis MJ Moyed HS. Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol 173: 5732–5739, (1991).
53. Black DS Irwin B Moyed HS. Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J Bacteriol 176: 4081–4091, (1994).
54. Korch SB Henderson TA Hill TM. Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol Microbiol 50: 1199–1213, (2003).
55. Keren I Shah D Spoering A Kaldalu N Lewis K. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli. J Bacteriol 186: 8172–8180, (2004).
56. Dorr T Vulic M Lewis K. Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol 8: e1000317, (2010).
57. Kim Y Wood TK. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun 391: 209–213, (2010).
58. Maisonneuve E Shakespeare LJ Girke M Gerdes K. Bacterial persistence by RNA endonucleases.
P Natl Acad Sci USA 108: 13206–13211, (2011).
59. Stewart PS Franklin MJ. Physiological heterogeneity in biofilms. Nat Rev Microbiol 6: 199–210, (2008).
91 60. Hall-Stoodley L Stoodley P. Developmental regulation of microbial biofilms. Curr Opin Biotechnol 13: 228–233, (2002).
61. Von Rosenvinge EC O'May G Macfarlane S Macfarlane GT Shirtliff ME. Microbial biofilms and gastrointestinal diseases. Pathog Dis 67: 25–38, (2013).
62. Mulcahy LR Isabella VM Lewis K. Pseudomonas aeruginosa biofilms in disease. Microb Ecol, (2013).
63. Bjarnsholt T. The role of bacterial biofilms in chronic infections. APMIS 136 (Suppl): 1–51, (2013).
64. Rybtke MT Jensen PO Hoiby N Givskov M Tolker-Nielsen T Bjarnsholt T. The Implication of Pseudomonas aeruginosa biofilms in infections. Inflamm Allergy-Drug Targets 10: 141–157, (2011).
65. Lewis K. Persister cells, dormancy and infectious disease. Nat Rev Microbiol 5:48–56, (2007).
66. Lewis K. Persister cells. Annu Rev Microbiol 64: 357–372, (2010).
67. Ren D Bedzyk L Thomas SM Ye RW Wood TK. Gene expression in Escherichia coli biofilms. Appl Microbiol Biotechnol 64: 515–524, (2004).
68. Kasari V Kurg K Margus T Tenson T Kaldalu N.The Escherichia coli mqsR and ygiT genes encode a new toxin–antitoxin pair. J Bacteriol 192: 2908–2919, (2010).
69. Barrios AFG Zuo R Yang L Bentley WE Thomas K Gonza F Hashimoto Y Wood TK. Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). J Bacteriol 188: 305–316, (2006).
70. Soo VWC Wood TK. Antitoxin MqsA represses curli formation through the master biofilm regulator CsgD. Sci Rep 3: 3186, (2013).
71. Wang X Lord DM Cheng HY et al. A novel type V TA system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol 8: 855–861, (2013).
72. Kim Y Wang X Ma Q Zhang X-S Wood TK. Toxin–antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae. J Bacteriol 191: 1258–1267, (2009).
73. Kolodkin-Gal I Verdiger R Shlosberg-Fedida A Engelberg-Kulka H. A differential effect of E. coli toxin–antitoxin systems on cell death in liquid media and biofilm formation. PLoS One 4: e6785, (2009).
92 74. Bayles KW. Bacterial programmed cell death: making sense of a paradox. Nat Rev Microbiol 12:
63–69, (2014).
75. Rice KC Mann EE Endres JL Weiss EC Cassat JE Smeltzer MS Bayles JW. The cidA murein hydrolase regulator contributes to DNA release and biofilm production in Staphylococcus aureus. P Natl Acad Sci USA 104: 8113–8118, (2007).
76. Mitchell HL Dashper SG Catmull DV Paolini RA Cleal SM Slakeski N Tan KH Reynolds EC.
Treponema denticola biofilm-induced expression of a bacteriophage, toxin–antitoxin systems and transposases. Microbiology 156: 774–788, (2010).
77. Theunissen S De Smet L Dansercoer A Motte B Coenye T Van Beeumen JJ Devreese B Savvides SN Vergauwen B.The 285 kDa Bap/RTX hybrid cell surface protein (SO4317) of Shewanella oneidensis MR-1 is a key mediator of biofilm formation. Res Microbiol 161: 144–152, (2010).
78. Zhao J Wang Q Li M Heijstra BD Wang S Liang Q Qi Q. Escherichia coli toxin gene hipA affects biofilm formation and DNA release. Microbiology 159: 633–640, (2013).
79. Georgiades K Raoult D. Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin–antitoxin modules. PLoS One 6: e17962, (2011).
80. Ma Z Geng J Yi L Xu B Jia R Li Y Meng Q Fan H Hu S. Insight into the specific virulence related genes and toxin–antitoxin virulent pathogenicity islands in swine streptococcosis pathogen Streptococcus equi ssp. zooepidemicus strain ATCC35246. BMC Genomics 14: 377, (2013).
81. Sayeed S Reaves L Radnedge L Austin S. The stability region of the large virulence plasmid of Shigella flexneri encodes an efficient postsegregational killing system. J Bacteriol 182: 2416–2421, (2000).
82. Hurley JM Woychik N. Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. J Biol Chem 284: 18605–18613, (2009).
83. Ren D Walker AN Daines D. Toxin–antitoxin loci vapBC-1 and vapXD contribute to survival and virulence in nontypeable Haemophilus influenzae. BMC Microbiol 12: 263, (2012).
93 84. Audoly G Vincentelli R Edouard S Georgiades K Mediannikov O Gimenez G Socolovschi C Mège JL Cambillau C Raoult D. Effect of rickettsial toxin VapC on its eukaryotic host. PLoS One 6: e26528, (2011).
85. Rothenbacher FP Suzuki M Hurley JM Montville TJ Kirn TJ Ouyang M Woychik NA. Clostridium difficile MazF toxin exhibits selective, not global, mRNA cleavage. JBacteriol 194: 3464–3474, (2012).
86. Moritz EM Hergenrother PJ. Toxin–antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci. P Natl Acad Sci USA 104: 311–316, (2007).
87. Sayed N Nonin-Lecomte S Réty S Felden B. Functional and structural insights of a Staphylococcus aureus apoptotic-like membrane peptide from a toxin–antitoxin module. J Biol Chem 287: 43454–
43463, (2012).
88. Park SJ Son WS Lee B-J. Structural overview of toxin–antitoxin systems in infectious bacteria: a target for developing antimicrobial agents. Biochim Biophys Acta 1834: 1155–1167, (2013).
89. Mandal S Moudgil M Mandal SK. Rational drug design. Eur J Pharmacol 625: 90–100, (2009).
90. Lewis K. Recover the lost art of drug discovery. Nature 485: 439–440, (2012).
91. Lewis K. Platforms for antibiotic discovery. Nat Rev Drug Discov 12: 371–387, (2013).
92. Conlon BP Nakayasu ES Fleck LE LaFleur MD Isabella VM Coleman K Leonard SN Smith RD Adkins JN Lewis K.Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature 503: 365–
370, (2013).
93. Trovatti E Cotrim CA Garrido SS Barros RS Marchetto R. Peptides based on CcdB protein as novel inhibitors of bacterial topoisomerases. Bioorg Med Chem Lett 18: 6161–6164, (2008).
94. Brielle, R.; Pinel-Marie, M.L.; Felden, B. Linking bacterial type I toxins with their actions. Curr.
Opin. Microbiol, 30, 114–121 (2016).
95. Gerdes, K.;Wagner, E.G. RNA antitoxins. Curr. Opin. Microbiol, 10, 117–124, (2007).
96. Brantl, S.; Jahn, N. sRNAs in bacterial type I and type III toxin–antitoxin systems. FEMS Microbiol.
Rev., 39, 413–427, (2015).
94 97. Wessner, F.; Lacoux, C.; Goeders, N.; Fouquier d’Herouel, A.; Matos, R.; Serror, P.; Van Melderen, L.; Repoila, F. Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen Enterococcus faecalis. RNA Biol, 12, 1099–1108, (2015).
98. Dufourc, E.J; Buchoux, S. Toupe, J. ; Sani, M.A. ; Jean-Francois, F. ; Khemtemourian, L. ; Grelard, A. ; Loudet-Courreges, C. ; Laguerre, M.; Elezgaray, J.; et al. Membrane interacting peptides: From killers to helpers. Curr. Protein Pept. Sci., 13, 620–631, (2012).
99. Gerdes K Poulsen LK Thisted T Nielsen AK Martinussen J Andreasen PH. The hok killer gene family in gram-negative bacteria. New Biol 2: 946–956, (1990).
100. Weaver, K.E.; Tritle, D.J. Identification and characterization of an Enterococcus faecalis plasmid pAD1 encoded stability determinant which produces two small RNA molecules necessary for its function. Plasmid, 32, 168–181, (1994).
101. Weaver, K.E.; Reddy, S.G.; Brinkman, C.L.; Patel, S.; Bayles, K.W.; Endres, J.L. Identification and characterization of a family of toxin–antitoxin systems related to the Enterococcus faecalis plasmid pAD1 par addiction module. Microbiology, 155, 2930–2940, (2009).
102. Greenfield, T.J.; Weaver, K.E. Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 50 and 30 ends of the RNAs. Mol. Microbiol., 37, 661–670, (2000).
103. Chukwudi, C.U.; Good, L. The role of the hok/sok locus in bacterial response to stressful growth conditions. Microb. Pathog, 79, 70–79, (2015).
104. Verstraeten, N.; Knapen, W.J.; Kint, C.I.; Liebens, V.; van den Bergh, B.; Dewachter, L.; Michiels, J.E.; Fu, Q.; David, C.C.; Fierro, A.C.; et al. Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance. Mol. Cell, 59, 9–21, (2015).
105. Verstraeten et al., 2019
106. Fozo, E.M.; Kawano, M.; Fontaine, F.; Kaya, Y.; Mendieta, K.S.; Jones, K.L.; Ocampo, A.; Rudd, K.E.; Storz, G. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol.
Microbiol., 70, 1076–1093, (2008).
95 107. Kawano, M.; Reynolds, A.A.; Miranda-Rios, J.; Storz, G. Detection of 50- and 30-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res., 33, 1040–1050, (2005).
108. Vogel, J.; Argaman, L.;Wagner, E.G.; Altuvia, S. The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol., 14, 2271–2276, (2004).
109. Kawano, M.; Oshima, T.; Kasai, H.; Mori, H. Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol. Microbiol., 45, 333–349, (2002).
110. Weel-Sneve, R.; Kristiansen, K.I.; Odsbu, I.; Dalhus, B.; Booth, J.; Rognes, T.; Skarstad, K.; Bjoras, M. Single transmembrane peptide DinQ modulates membrane-dependent activities. PLoS Genet.
(2013).
111. Fozo, E.M. New type I toxin–antitoxin families from “wild” and laboratory strains of E. coli: Ibs-Sib, ShoB-OhsC and Zor-Orz. RNA Biol., 9, 1504–1512, (2012).
112. Kawano M Aravind L Storz G. An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64: 738–754, (2007).
113. Guo, Y.; Quiroga, C.; Chen, Q.; McAnulty, M.J.; Benedik, M.J.;Wood, T.K.;Wang, X. RalR (a DNase) and RalA (a small RNA) form a type I toxin–antitoxin system in Escherichia coli. Nucleic Acids Res., 42, 6448–6462, (2014).
114. Silvaggi, J.M.; Perkins, J.B.; Losick, R. Small untranslated RNA antitoxin in Bacillus subtilis. J.
Bacteriol., 187, 6641–6650, (2005).
115. Durand, S.; Jahn, N.; Condon, C.; Brantl, S. Type I toxin-antitoxin systems in Bacillus subtilis.
RNA Biol., 9, 1491–1497, (2012).
116. Pinel-Marie, M.L.; Brielle, R.; Felden, B. Dual toxic-peptide-coding Staphylococcus aureus RNA under antisense regulation targets host cells and bacterial rivals unequally. Cell Rep., 7, 424–435, (2014).
117. Aizenman E Engelberg-Kulka H Glaser G. An Escherichia coli chromosomal “addiction module”
regulated by 3,5’-bispyrophosphate: a model for programmed bacterial cell death. P Natl Acad Sci USA 93: 6059–6063, (1996).
96 118. Van Melderen L. ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. J Biol Chem 271: 27730–27738, (1996).
119. Brown BL Lord DM Grigoriu S Peti W Page R. The Escherichia coli toxin MqsR destabilizes the transcriptional repression complex formed between the antitoxin MqsA and the mqsRA operon promoter. J Biol Chem 288: 1286–1294, (2013).
120. Masuda Y Miyakawa K Nishimura Y Ohtsubo E. chpA and chpB, Escherichia coli chromosomal homologs of the pem locus responsible for stable maintenance of plasmid R100. J Bacteriol 175:
6850–6856, (1993).
121. Engelberg-Kulka H Hazan R Amitai S. MazEF: a chromosomal toxin–antitoxin module that triggers programmed cell death in bacteria. J Cell Sci 118: 4327–4332, (2005).
122. Zhang Y Zhang J Hoeflich KP Ikura M Qing G Inouye M. MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell 12: 913–923, (2003).
123. Kolodkin-Gal I Hazan R Gaathon A Carmeli S Engelberg-Kulka H,A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science 318: 652–
655, (2007).
124. Park SJ Son WS Lee B-J. Structural overview of toxin–antitoxin systems in infectious bacteria: a target for developing antimicrobial agents. Biochim Biophys Acta 1834: 1155–1167, (2013).
125. Cook GM Robson JR Frampton RA McKenzie J Przybilski R Fineran PC Arcus VL. Ribonucleases in bacterial toxin–antitoxin systems. Biochim Biophys Acta 1829: 523–531, (2013).
126. Winther KS Brodersen DE Brown AK Gerdes K. VapC20 of Mycobacterium tuberculosis cleaves the Sarcin-Ricin loop of 23S rRNA. Nat Commun 4: 2796, (2013).
127. Schumacher MA Piro KM Xu W Hansen S Lewis K Brennan RG. Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 323: 396–401, (2009).
128. Schumacher MA Min J Link TM et al. Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance. Cell Rep 2: 518–525, (2012).
129. Correia FF D'Onofrio A Rejtar T Li L Karger BL Makarova K Koonin EV Lewis K. Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J Bacteriol 188: 8360–8367, (2006).
97 130. Shao Y Harrison EM Bi D Tai C He X Ou H-Y Rajakumar K Deng Z. ADB: a webbased resource for Type 2 toxin–antitoxin loci in bacteria and archaea. Nucleic Acids Res 39: D606–D611, (2011).
131. Short FL Pei XY Blower TR Ong S-L Fineran PC Luisi BF Salmond GPC. Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot. P Natl Acad Sci USA 110: E241–E249, (2013).
132. Fineran PC Blower TR Foulds IJ Humphreys DP Lilley KS Salmond GPC. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin–antitoxin pair. P Natl Acad Sci USA 106:
894–899, (2009).
133. Francesca L. Short, Chidiebere A., William R. Broadhurst & George P. C. Salmond. The bacterial Type III toxin-antitoxin system, ToxIN, is a dynamic protein-RNA complex with stability-dependent antiviral abortive infection activity. Scientific Report, 1013-846, (2018).
134. Blower TR Pei XY Short FL Fineran PC Humphreys DP Luisi BF Salmond GPC. A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nat Struct Mol Biol 18: 185–190, (2011).
135. Samson, J.E.; Spinelli, S.; Cambillau, C.; Moineau, S. Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin–antitoxin system. Mol. Microbiol, 87, 756–768, (2013).
136. Masuda H Tan Q Awano N Wu K-P Inouye M. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol Microbiol 84: 979–989, (2012).
137. Arbing, M.A.; Handelman, S.K.; Kuzin, A.P.; Verdon, G.;Wang, C.; Su, M.; Rothenbacher, F.P.;
Abashidze, M.; Liu, M.; Hurley, J.M.; et al. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Structure, 18, 996–1010, (2010).
138. Wang, X.; Lord, D.M.; Cheng, H.Y.; Osbourne, D.O.; Hong, S.H.; Sanchez-Torres, V.; Quiroga, C.;
Zheng, K.; Herrmann, T.; Peti,W.; et al. A new type V toxin–antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol, 8, 855–861 (2012).
139. Wang X Lord DM Cheng HY et al. A novel type V TA system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat Chem Biol 8: 855–861, (2013).
98 140. Aakre, C.D.; Phung, T.N.; Huang, D.; Laub, M.T. A bacterial toxin inhibits DNA replication elongation through a direct interaction with the beta sliding clamp. Mol. Cell, 52, 617–628, (2013).
141. Darfeuille F, Unoson C, Vogel J, Wagner EG: An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell, 26:381-392, (2007).
142. Jahn N, Brantl S: One antitoxin-two functions: SR4 controls toxin mRNA decay and translation.
Nucleic Acids Res, 41:9870-9880, (2013).
143. Jahn N, Brantl S, Strahl H: Against the mainstream: the membrane-associated type I toxin BsrG from Bacillus subtilis interferes with cell envelope biosynthesis without increasing membrane permeability. Mol Microbiol (2015).
144. Gerdes K, Rasmussen PB, Molin S: Unique type of plasmid maintenance function:
postsegregational killing of plasmid-free cells. Proc Natl Acad Sci U S A, 83:3116-3120, (1986).
145. Gerdes K Wagner EGH. RNA antitoxins. Curr Opin Microbiol 10: 117–124, (2007).
146. Poulsen LK, Larsen NW, Molin S, Andersson P: A family of genes encoding a cell-killing function may be conserved in all gram- negative bacteria. Mol Microbiol, 3:1463-1472, (1989).
147. Pedersen K, Gerdes K: Multiple hok genes on the chromosome of Escherichia coli. Mol Microbiol, 32:1090-1102, (1999).
148. Wilmaerts, D. et al. The persistence-inducing toxin HokB forms dynamic pores that cause ATP leakage. mBio 9 (2018).
149. Brinkman CL, Bumgarner R, Kittichotirat W, Dunman PM, Kuechenmeister LJ, Weaver KE:
Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin–
antitoxin system toxin. J Bacteriol, 195:156-166, (2013).
150. Dintner S, Staron A, Berchtold E, Petri T, Mascher T, Gebhard S: Coevolution of ABC transporters and two-component regulatory systems as resistance modules against antimicrobial peptides in Firmicutes Bacteria. J Bacteriol, 193:3851-3862, (2011).
151. Weaver KE: The par toxin–antitoxin system from Enterococcus faecalis plasmid pAD1 and its chromosomal homologs. RNA Biol, 9:1498-1503, (2012).
152. Kawano M: Divergently overlapping cis-encoded antisense RNA regulating toxin–antitoxin systems from E. coli: hok/sok, ldr/rdl, symE/symR. RNA Biol, 9:1520-1527, (2012).